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Data and code for reproducing the deep learning framerwork described in CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters
Here, this study revisits the three-point sampling of the simplified Butler-Volmer equation to address the limitations of strong potentiodynamic polarization, which can introduce irreversible damage and uncertainty in corrosion analysis. The method extracts electrochemical kinetic parameters while minimizing polarization effects, evaluates noise sensitivity relative to overpotential, and accounts for errors from signal noise, OCP drift, ohmic resistance, and mass-transfer constraints. Verified against the Tafel extrapolation method for aluminum corrosion across a wide pH range, this low-polarization approach enables accurate evaluations with specific error estimates, offering a robust alternative to linear polarization resistance methods that assume constant Tafel slopes.
Triaminotrinitrobenzene-based high explosives such as LX-17 offer high energy density and exceptional safety, yet their long-term aging behavior at low temperatures remains poorly understood. In this study, several legacy and new production lots of LX-17 were subjected to accelerated aging experiments below 100°C, during which the formation rate of the initial degradation product, monofurazan (F1), was monitored. Kinetic analysis was performed using a sample-age-aware computational approach, yielding activation energy estimates of 82–91 kJ mol −1 for the low-temperature initiation step—markedly lower than the ∼200 kJ mol −1 associated with high-temperature thermal decomposition. Extrapolation from established cookoff models supports the conclusion that the dominant degradation mechanism at low temperatures differs from that at high temperatures. In conclusion, our results provide a unified kinetic framework that bridges the gap between in-service conditions and high-temperature damage.
Here, the goal of the present work was to provide the necessary reaction emulation information to enable detailed process simulation of a chemical looping H 2 production system from fossil fuels using CaFe 2 O 4 . This specifically pertained to the necessary kinetic data, reaction model development, and model rate parameters required for reaction emulation in both reducing and oxidizing environments. A logical methodology was defined, which included discretization of the reaction network, establishing a core model for reaction emulation that could be adapted based on the system phenomena, and development of a rate parameter regression tool designed around the core model. An extensive array of data sets was acquired by which parametric regressions were performed. The work presented and tabulated a comprehensive set of rate parameters for the reduction and oxidation reactions of CaFe 2 O 4 and descendent phases of Ca 2 Fe 2 O 5 , FeO, Fe 3 O 4 , Fe, and CaO to emulate reaction behavior in a looping-based process environment. This included direct reduction using CH 4 , H 2 , and CO, and direct oxidation reactions with steam, CO 2 and O 2 . Dynamic equilibrium was quantified for reactions that could utilize H 2 O and CO 2 as soft oxidants to re-saturate lattice oxygen in the depleted structure/phases. The kinetics associated with the oxidative mechanisms with the soft oxidants were quantified and compared to those of the reducing counterparts. The analysis provided critical insight to emulate reactions for a process that seeks to use natural gas (NG) or other fossil fuels as a direct reductant for the end goal of H 2 production.
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The nodal diffusion method is one of the most widely used approaches in modern reactor analysis. In the nodal diffusion method, a coarse multi-group set of “homogenized” parameters is constructed such that the complex geometry of a reactor core along with the energy dependence of neutron and gamma ray cross sections in a nuclear reactor are conserved in the simpler geometry. The homogenization is typically done on a fuel assembly level as is the case in the DIF3D code developed at Argonne National Laboratory. The nodal methodology is used primarily to predict fuel cycle behavior of nuclear systems of which there is a substantial amount of validation in the literature. Another use of the nodal method is to obtain reactivity coefficients and kinetics parameters for use in a safety analysis of a given nuclear reactor. While there are many ways to obtain reactivity worth and kinetics parameters, the work presented in this manuscript is unique as it provides the user with the ability to compute reactivity worths, kinetics parameters, and cross section sensitivities with a Cartesian and hexagonal geometry based transport code. This manuscript serves as a single manual for two separate codes: VARI3D and PERSENT. The VARI3D code (VARIational 3D) is based upon the classic finite difference diffusion theory solver available in DIF3D. The PERSENT code (PERturbation and SENitivity for Transport) is based upon the variational nodal method employed in DIF3D termed VARIANT. The VARIANT solver was added to DIF3D in 1995 and has seen continued development and use for the last 18 years. Because VARI3D primarily uses deprecated coding practices, rather than incorporating the perturbation and sensitivity treatments for transport within VARI3D, a new coding development was built using modern Fortran coding. The primary purpose of this manual is to describe the theory behind PERSENT (and by convenience, that of VARI3D) and discuss the input and output of PERSENT along with giving potential users an idea of how to use it. While this manuscript does describe the input and output of VARI3D, the PERSENT code is intended to be the replacement capability of VARI3D as PERSENT can generate nearly identical (if not superior) diffusion theory results. In this manuscript, the relevant aspects of generalized perturbation theory and exact perturbation theory that apply to both VARI3D and PERSENT are covered. The input and output of VARI3D is displayed by excerpting several of the example problems. Similarly, the input and output of PERSENT is displayed along with tips on how best to use the code. Note that the input and output of the inhomogeneous solver wrapped around DIF3D (DIF3D_IFS) is also discussed as it is needed to carry out some of the sensitivities in PERSENT such as reaction rate ratios. This manuscript describes several perturbation and sensitivity problems, and the results computed using PERSENT. From these sections, potential users should find that PERSENT provides not only the typical tables of numbers desired in perturbation and sensitivity analysis work, but also can visually plot the result for a more thorough understanding of the space and energy distribution (Section 5). Overall, PERSENT is observed to produce accurate reactivity worths and sensitivities for the displayed set of test problems and clearly demonstrates the need to have a transport-based sensitivity capability as evident from the thousands of percent errors observed in the 21-group hexagonal fast reactor problem (covered in Section 7). The uncertainty calculation capability is described in Section 3 and demonstrated in Section 7.
Visible photon fluxes can influence the rate and selectivity of heterogeneously catalyzed reactions on metal nanoparticle surfaces. Models describing the influence of photon fluxes have typically introduced photon flux dependent apparent thermal kinetic parameters (reaction orders, activation energies, binding energies, etc.). This has relied on empirical fitting of reaction rate data, making mechanistic interpretations of how photon fluxes influence elementary step rates challenging and inconsistent with fundamental descriptions of photochemistry on metal surfaces developed from surface science studies. Using the CO adsorption–desorption quasi-equilibrium reaction on Pt/Al 2 O 3 catalysts as a model system, we measured steady state adsorbed CO (CO*) coverages under isothermal and isobaric (1 mbar CO) conditions as a function of temperature (473–573 K) and of 440 nm photon flux ((0.1–5.2) × 10 3 # hv Pt site –1 s –1 ) using in situ IR spectroscopy. Steady state CO* coverage on Pt was photon flux dependent with increasing photon flux causing decreasing coverage, consistent with photons driving CO* desorption rates faster than thermal CO* desorption rates. However, photon flux dependent CO* coverages were essentially temperature independent, inconsistent with models that describe photon effects using perturbations to apparent thermal kinetic parameters. Instead, 120 steady state CO* coverages as a function of temperature and photon flux are quantitatively described by a kinetic model in which the overall desorption rate is a summation of independent thermal and photon induced CO* desorption rates. Site-resolved analysis reveals distinct kinetic parameters for photon driven desorption of CO* from well-coordinated, under-coordinated, and highly under-coordinated Pt sites, with temperature-dependent apparent quantum efficiencies (AQE) consistent with temperature dependence of vibrational quanta distribution of adsorbed CO. The rigorous kinetic rate laws for independent photon and thermal driven pathways allow for predictive modeling of the influence of photon fluxes on the rates of CO* desorption under catalytic conditions. Further, the analysis provides evidence that steady state continuous wave photon fluxes can drive desorption/adsorption reactions on metal surfaces out of thermal equilibrium, reconciling surface science observations of molecular photodesorption with applied catalysis. The work establishes a general kinetic framework to be considered for photon driven processes on metals, and defines catalyst, reaction, and photon flux characteristic design principles for breaking Sabatier limitations.
Temperature-controlled, time-resolved picosecond electron pulse radiolysis was utilized to measure the rate of reaction between the solvated electron (eS–) and dissolved oxygen in n-dodecane solutions from 2.5 to 40 °C for the first time. At 20.0 °C, the reaction rate was determined to be k(eS– + O2) = (4.54 ± 0.21) × 1010 M-1 s-1, with an activation energy of Ea = 14.4 ± 1.3 kJ mol-1. These newly determined kinetic parameters are important for predicting and managing the effects of aerated environments on the degradation of organic solvents used in nuclear fuel reprocessing technologies.
Microkinetic models for catalytic systems require estimation of many thermodynamic and kinetic parameters that can be calculated for isolated species and transition states using ab initio methods. However, the presence of nearby coadsorbates on the surface can dramatically alter these thermodynamic and kinetic parameters causing them to be dependent on species coverage fractions. As there are combinatorially many coadsorbed configurations on the surface, computing the coverage dependence of these parameters is far less straightforward. We present a framework for generating and applying machine learning models to predict coverage-dependent parameters for microkinetic models. Our toolkit enables automatic calculation and evaluation of coadsorbed configurations allowing us to sample 2,000 coadsorbed adsorbates and transition states (TSs) for a diverse set of 9 reactions on Cu(111), a challenging surface, with four possible coadsorbates. This dataset was then used to train subgraph isomorphic decision trees (SIDTs) to predict the stability and association energy of configurations. We were able to achieve mean absolute errors (MAEs) of 0.106 eV on adsorbates, 0.172 eV on TSs, and due to natural error cancellation in SIDTs for relative properties, 0.130 eV on reaction energies and 0.180 eV on activation barriers. In conclusion, we describe how to use these models to predict coverage-dependent corrections for adsorbates and TSs and demonstrate on H*, HO*, and O* comparing the generated SIDT model with an iteratively refined version.
Ongoing commercial design activities require a thorough verification of the Argonne Reactor Computation codes be performed. DIF3D is central to this system and substantial work has been done to verify its accuracy on several identified commercial needs. This manuscript details the verification work done on PERSENT which relies upon the DIF3D code for its forward and adjoint flux solution. Previous work identified the PERSENT features required to be verified to support commercial design activities, features of which are generally applicable to hexagonal-Z fast reactor designs. The scope of this verification effort includes verifying PERSENT’s ability to correctly calculate four key quantities: perturbation worth distributions, kinetics parameters, sensitivity coefficients, and cross section uncertainty quantification. This manuscript provides the verification tasks and their results with respect to these quantities needed for commercial design activities. For the perturbation worth distributions, hand calculations are deployed to verify the PERSENT calculated results. Similarly, hand calculation of the PERSENT computed kinetics parameters is also used to verify the PERSENT results. In both of these, the input to PERSENT is manipulated to ensure the hand calculation exactly matches the equations PERSENT is calculating. The sensitivity coefficients involve calculating the derivatives of a parameter (such as reactivity worth), with respect to the cross section data. Direct finite difference calculations with DIF3D are used to verify the PERSENT calculated results. For the uncertainty quantification, manufactured input to PERSENT is used to allow an exact hand calculation to reproduce the PERSENT calculated results. The work detailed in this report verified that significant issues were identified for earlier versions of PERSENT for sensitivity coefficients which were corrected in this work and thus version 12.1.0 of PERSENT must be used to reproduce all of the verified work in this report.
Here, this study develops intrinsic methane oxidation kinetics for ultra-lean methane conditions in the presence of water over a highly active and stable PtPd–Mg/θ-Al 2 O 3 catalyst. Comprehensive laboratory experiments were conducted over a wide range of methane concentrations (150–1200 ppm CH 4 ), water contents (1–5% H 2 O), and industrially relevant space velocities (80,000 ≤ GHSV ≤ 160,000 h -1 ). These systematic experiments informed a two-dimensional, axisymmetric, multiscale reactor model that was used to develop and validate methane oxidation kinetics under practically relevant conditions, including non-isothermal operation and high conversion regimes. Combined experimental and modeling results revealed significant intraparticle diffusion resistance and transport-induced reaction exotherm at elevated temperatures, which limited catalyst utilization despite high intrinsic activity. These transport effects were explicitly incorporated into the reactor model, enabling accurate estimation of intrinsic kinetic parameters without reliance on conventional effectiveness-factor corrections. The resulting kinetic model successfully captured both kinetically controlled and mass-transfer-limited regimes and reliably predicted CH 4 conversion across broad ranges of temperature, methane concentration, and water content
The kinetics and thermodynamics of elementary reaction steps involved in the catalytic reduction of protons to hydrogen define the reaction landscape for catalysis. The mechanisms can differ in the order of the elementary proton transfer, electron transfer, and bond-forming steps and can be further differentiated by the sites at which protons and electrons localize. Access to fully elucidated mechanistic, kinetic, and thermochemical details of molecular catalysts is crucial to facilitate the development of new catalysts that operate with optimal efficiency, selectivity, and durability. The mechanism by which a catalyst operates, as well as the kinetics and thermodynamics associated with the individual steps, can often be accessed through electroanalytical studies. Here, this Account details the application of cyclic voltammetry to interrogate reaction mechanisms and quantify the kinetics and thermodynamics of elementary reaction steps for a series of molecular catalysts that mediate electrochemical proton reduction. I distinguish the limiting scenarios wherein a catalyst operates under kinetic control vs thermodynamic control, with a focus on detecting how cyclic voltammetry features shift with proton source strength and concentration, as well as scan rate. For systems that operate under kinetic control, catalytic currents are observed at, or slightly positive toward, the formal potential for the redox process that triggers catalysis. Under thermodynamic control, catalytic responses shift as a function of the proton source pKa and effective pH of the solution. After drawing this distinction, we introduce the appropriate voltammetry experiments and accompanying analytical expressions for extracting key metrics from the data. To illustrate analytical strategies to quantify elementary reaction steps of catalysts operating under kinetic control, I describe our studies of proton reduction catalysts Co(dmgBF 2 ) 2 (CH 3 CN) 2 (dmgBF 2 = difluoroboryl-dimethylglyoxime) and [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ (P 2 Ph N 2 Ph = 1,5-phenyl-3,7-phenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, peak shift analysis, foot-of-the-wave analysis, and plateau current analysis are applied to data sets wherein voltammetric response are recorded as a function of catalyst concentration, proton source concentration, proton source strength, and scan rate to quantify rate constants for elementary proton transfer and bond-forming steps in a catalytic cycle. Further, the case study of [Ni(P 2 Ph N 2 Ph ) 2 ] 2+ illustrates how complementary spectroscopic methods can bolster the mechanistic assignment. Collectively, these two studies showcase how detailed mechanistic studies inform on rate-limiting elementary steps in catalysis and other key processes underpinning catalysis. Second, I present analytical strategies to interrogate catalysts operating under thermodynamic control, centered on the case study of [Ni II (P 2 Ph N 2 Bn ) 2 ] 2+ (P 2 Ph N 2 Bn = 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane). Here, the application of nonaqueous Pourbaix theory to extract thermodynamic information is introduced, and the construction of a coupled Pourbaix diagram is detailed. This study identifies ligand-based protonation as the key process that places catalysis under thermodynamic control and influences the reaction mechanism. Together, the work detailed in this Account showcases the utility of electroanalytical methods to disentangle complex reaction mechanisms and extract key thermochemical and kinetic parameters for elementary steps of catalysis. Through detailed presentation of the key analytical expressions that underpin these analyses, this Account seeks to facilitate the adoption of cyclic voltammetry by the community to fully extract kinetic, thermochemical, and mechanistic information on electrochemical small-molecule activation.
Here, this study presents the first intrinsic kinetic model for the single-step conversion of ethanol to butene-rich olefins over bifunctional Cu-Y/Beta catalysts, addressing a critical gap in the design and scale-up of Sustainable Aviation Fuel (SAF) processes. The reaction network comprises ten global steps involving dehydrogenation, aldol condensation, hydrogenation, and dehydration reactions, distributed across Cu and rare-earth (Y) active sites. The model incorporates dual-site functionality (Cu and Y site) and explicitly accounts for key intermediates such as crotonaldehyde and butanal. Reaction rates are formulated using Langmuir–Hinshelwood–Hougen–Watson (LHHW) kinetics. Kinetic parameters are extracted by fitting the model to lab-scale packed-bed reactor data across a wide range of temperatures and space velocities, demonstrating strong agreement in ethanol conversion and product selectivity. The reaction kinetics developed in this work provide a foundational basis for constructing reactor models that enable process optimization and scale-up of ethanol-to-jet fuel technologies.
The research presented in this article describes progress in applying stochastic methods, uncertainty quantification, parametric studies, and variance-based sensitivity analysis (also known as Sobol sensitivity analysis) to a full-core model of a nuclear thermal propulsion (NTP) system simulated via the radiation transport code Griffin to simulate neutronics. Our goal is to develop a reduced-order (surrogate) model that can be rapidly sampled with perturbations to multiple input parameters. In this NTP system, reactivity and power feedback affect the rotation of control drums (CDs), which is itself controlled by a hybrid proportional-integral-derivative (PID) controller actuated by the power demand and reactivity feedback from the numerical model. This model uses reactor kinetic feedback (mean generation time [Λ] and effective delayed neutron fraction [ β eff ] from a transient Griffin simulation executed via Griffin’s improved quasi-static solver to provide the kinetic parameters) as inputs to functions that control the CD rotation angle. By investigating numerous stochastic approaches, we developed a dual-purpose surrogate model of the NTP system, using polynomial regression in the Multiphysics Object-Oriented Simulation Environment (MOOSE) Stochastic Tools Module (STM). The trained model can be rapidly sampled while simultaneously perturbing various input parameters, such as coefficients on the PID control or temperature (directly affecting the neutron cross section). The surrogate model delivers accurate (within 5%) results at speeds orders of magnitude faster (minutes, not days of computational time) than the base model. Once the surrogate model has been trained, distributions of the uncertain parameters can be changed at will to investigate the effects of perturbing multiple inputs as well as the effects of these inputs on the model output. For example, coefficients used in the PID control system may vary due to some type of physical interference, or uncertainty may exist in the temperature of the neutron cross sections in various regions of the reactor. A distribution can be placed on these parameters, and operational boundaries can be determined. The goal of this work is to support development of an advanced control system for operating CDs in a functioning NTP system. This work is a scoping study of the MOOSE STM.
An Arrhenius–Wescott–Stewart–Davis (AWSD) reactive burn model is applied to describe shock initiation and detonation properties of the HMX-based high explosive LX-04. The parameters in the model are calibrated to data from multiple sources. The thermodynamic equations of state used in the model are calibrated to a combination of thermochemical calculations for HMX and LX-04 as well as experimentally-measured cylinder expansion results for LX-04. The kinetic parameters are calibrated to velocity data from gas gun experiments performed using EDC-32—a high explosive with the same chemical composition as LX-04 but different structural properties, and scaled rate stick data for PBX 9012. The AWSD model is shown to accurately describe the shock initiation and propagation of LX-04. Very good agreement is observed between the available experimental data and the AWSD model output. The presented results constitute an accurate LX-04 reactive burn model for use in engineering-scale models and simulations.
Petroleum-based lubricants raise environmental concerns due to their non-biodegradability and toxicity, whereas biobased lubricants underperform owing to low thermal stability. This study examined and compared three vegetable oils, along with their chemically modified versions, to better understand their suitability as biolubricants. High oleic soybean oil (HOSOY), regular soybean oil (RSOY), and waste cooking oil (WCO) were subjected to chemical modification, where isopropyl groups were attached to the fatty acid chains of the oils to produce branched oils, i.e., b-HOSOY, b-RSOY, and b-WCO. The detailed kinetic study of each regular and modified sample was investigated using thermogravimetric analysis. The kinetic parameters, such as the activation energies, reaction rate, and pre-exponential factor, were generated via Friedman methods. The differential thermal gravimetric (DTG) analysis showed low volatilization at the onset temperature in each modified oil as compared with the unmodified samples under an oxidative environment. Furthermore, the comparative kinetic studies demonstrated the enhanced thermoxidative stability of the modified products relative to their unaltered counterparts. Among the tested oils, the b-RSOY showed an average activation energy of 325 kJ/mol, followed by the b-WCO: 300 kJ/mol and the b-HOSOY: 251 kJ/mol, indicating the most stable modified product under an oxidative environment. For all the samples, the pre-exponential factors were in good agreement with the activation energies, which validates that finding the pre-exponential components is crucial to the kinetic analysis.
Methodology is presented for non-destructive, optically-detected single nanoparticle (NP) mass spectrometry, with the goal of extracting surface reaction kinetics for single NPs at high temperatures. Methods for determining the NP charge, mass, and temperature as a function of time are discussed, and the data are used to extract both the absolute kinetics for mass change, as well as the efficiencies of the surface processes that cause them. Factors that contribute to the uncertainties in absolute and relative mass determination, and in the resulting kinetic parameters, are discussed. The method allows the NP-to-NP variations in initial reactivity to be measured directly, along with the time evolution of reactivity resulting from NP structural/compositional changes that occur under reaction conditions. The strengths and limitations of single nanoparticle mass spectrometry as a high temperature surface kinetics tool are discussed in the context of sublimation and O2 oxidation kinetics experiments for single hafnium (Hf) NPs at temperatures ranging above 2400 K. The Hf oxidation kinetics are compared to analogous oxidation experiments for silicon, graphite, and carbon black NPs. In all four cases, the oxidation chemistry was dominated by processes that result in net mass loss, and the distinct mechanisms responsible are discussed. All four NPs also eventually passivated, i.e., the efficiencies for oxidative etching decreased by at least two orders of magnitude, relative to the initial efficiencies. Furthermore, the passivation mechanisms, which are quite different for carbon, compared to silicon or hafnium, are discussed. Carbon NP passivation is attributed to structural isomerization leading to fully coordinated, fullerene-like NP surfaces, while for silicon and hafnium, passivation results from delayed formation of an oxide layer, triggered by accumulation of oxygen in the NP sub-surface region.
This project focused on addressing longstanding fundamental and experimental uncertainties on how dissolved organic substances (DOS) interact with metal oxide surface under environmentally relevant conditions. By leveraging a custom-built real-time, in-tandem flow adsorption microcalorimetry-UV-Vis/fluorescence spectroscopy platform, we characterized the binding energetics, kinetics and mechanistic pathways driving DOS-metal oxide interactions at temporal resolution on the order of 1-5 seconds. We studied a diverse suite of model organic compounds/substances – including monocarboxylates (e.g. acetate and benzoate), di-carboxylates (oxalate and succinate), amino acids, amino-based nanparticles and natural organic matter – interacting at the mineral-water interface of structurally- and/or chemically distinct metal oxides (including SiO2, boehmite, ferrihydrite, and γ-Al2O3). Our results indicated that DOS-metal oxide interactions are governed by multi-step reaction pathways, often switching between distinct, resolvable enthalpy- and entropy-driven non-electrostatic or electrostatic configurations. To quantify these interactions, we developed and implemented an analytical workflow that integrates peak deconvolution and Monte-Carlo based error propagation to determine site-specific thermodynamic and kinetic parameters for individual binding/debinding events. In addition to resolving apparent first-order rate constants of each event, we were able to quantify associated apparent equilibrium constants as well as free energy, enthalpy and entropy contribution to the activation and subsequent progression of the binding/debinding process across compounds, compound class and metal oxide surfaces. The kinetic-thermodynamic data produced in this study captured how the interplay between oxide surface reactivity and DOS molecular structure jointly drives binding-debinding dynamics. Notably, that at pH below PZC of the oxide surface, neutral species were heavily involved in monocarboxylate binding, while anionic species drove dicarboxylate binding. Also, that among amino acids 1) positional isomers show distinctive binding characteristics to each other while enantiomers show no significant differences in binding characteristics, 2) molecules that bind via outer-sphere complexation show a larger entropic shift between binding and debinding with no impact on oxide surface while 3) inner-sphere interactions increased anion exchange capacity of the oxide surface. The new insights and data from this work has great potential for improving predictive modeling of carbon dynamics and specifically organic-mineral interactions in environmental and industrial systems.